HP1β-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs

Epigenetics & Chromatin

Eva Bártová¹  Jaroslav Fulneček¹  Aleš Kovařík¹  Ivan Raška²  Pavel Matula³  Dmitry V Sorokin³  Stanislav Kozubek¹  Tereza Hrušková¹  Jana Suchánková¹  Soňa Legartová¹  Petra Sehnalová¹  Lenka Stixová¹ 

[1] Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic;Institute of Cellular Biology and Pathology, the First Faculty of Medicine, Charles University in Prague, Albertov 4, 128 01 Prague, Czech Republic;Faculty of Informatics, Masaryk University, Botanická 68a, 602 00 Brno, Czech Republic

关键词: UBF1;    Nucleolus;    Live-cell studies;    Irradiation;    DNA repair;    DNA-damage response;   

Others  :  1114997
DOI  :  10.1186/1756-8935-7-39

 received in 2014-04-11, accepted in 2014-12-12,  发布年份 2014

【 摘 要 】

Background

The repair of spontaneous and induced DNA lesions is a multistep process. Depending on the type of injury, damaged DNA is recognized by many proteins specifically involved in distinct DNA repair pathways.

Results

We analyzed the DNA-damage response after ultraviolet A (UVA) and γ irradiation of mouse embryonic fibroblasts and focused on upstream binding factor 1 (UBF1), a key protein in the regulation of ribosomal gene transcription. We found that UBF1, but not nucleolar proteins RPA194, TCOF, or fibrillarin, was recruited to UVA-irradiated chromatin concurrently with an increase in heterochromatin protein 1β (HP1β) level. Moreover, Förster Resonance Energy Transfer (FRET) confirmed interaction between UBF1 and HP1β that was dependent on a functional chromo shadow domain of HP1β. Thus, overexpression of HP1β with a deleted chromo shadow domain had a dominant-negative effect on UBF1 recruitment to UVA-damaged chromatin. Transcription factor UBF1 also interacted directly with DNA inside the nucleolus but no interaction of UBF1 and DNA was confirmed outside the nucleolus, where UBF1 recruitment to DNA lesions appeared simultaneously with cyclobutane pyrimidine dimers; this occurrence was cell-cycle-independent.

Conclusions

We propose that the simultaneous presence and interaction of UBF1 and HP1β at DNA lesions is activated by the presence of cyclobutane pyrimidine dimers and mediated by the chromo shadow domain of HP1β. This might have functional significance for nucleotide excision repair.

【 授权许可】

   
2014 Stixová et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Boulon S, Westman BJ, Hutten S, Boisvert FM, Lamond AI: The nucleolus under stress. Mol Cell 2010, 40(2):216-227.
• [2]Lindström MS, Latonen L: The nucleolus as a stress response organelle. In Proteins of the Nucleolus: Regulation, Translocation, and Biomedical Function. Edited by O’Day DH, Catalano A. Dordrecht: Springer; 2013:251-273.
• [3]Moore HM, Bai B, Boisvert FM, Latonen L, Rantanen V, Simpson JC, Pepperkok R, Lamond AI, Laiho M: Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation. Mol Cell Proteomics 2011, 10(10):M111 009241.
• [4]Blander G, Zalle N, Daniely Y, Taplick J, Gray MD, Oren M: DNA damage-induced translocation of the Werner helicase is regulated by acetylation. J Biol Chem 2002, 277(52):50934-50940.
• [5]Scott M, Bonnefin P, Vieyra D, Boisvert FM, Young D, Bazett-Jones DP, Riabowol K: UV-induced binding of ING1 to PCNA regulates the induction of apoptosis. J Cell Sci 2001, 114(19):3455-3462.
• [6]Rubbi CP, Milner J: Disruption of the nucleolus mediates stabilization of p53 in response to DNA damage and other stresses. EMBO J 2003, 22(22):6068-6077.
• [7]Kurki S, Peltonen K, Latonen L, Kiviharju TM, Ojala PM, Meek D, Laiho M: Nucleolar protein NPM interacts with HDM2 and protects tumor suppressor protein p53 from HDM2-mediated degradation. Cancer Cell 2004, 5(5):465-475.
• [8]Foltánková V, Legartová S, Kozubek S, Hofer M, Bártová E: DNA-damage response in chromatin of ribosomal genes and the surrounding genome. Gene 2013, 522(2):156-167.
• [9]Kruhlak M, Crouch EE, Orlov M, Montaño C, Gorski SA, Nussenzweig A, Misteli T, Phair RD, Casellas R: The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature 2007, 447(7145):730-734.
• [10]Boisvert FM, van Koningsbruggen S, Navascués J, Lamond AI: The multifunctional nucleolus. Nat Rev Mol Cell Biol 2007, 8(7):574-585.
• [11]Raska I, Shaw PJ, Cmarko D: New insights into nucleolar architecture and activity. Int Rev Cytol 2006, 255:177-235.
• [12]Sirri V, Urcuqui-Inchima S, Roussel P, Hernandez-Verdun D: Nucleolus: the fascinating nuclear body. Histochem Cell Biol 2008, 129(1):13-31.
• [13]Shav-Tal Y, Blechman J, Darzacq X, Montagna C, Dye BT, Patton JG, Singer RH, Zipori D: Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol Biol Cell 2005, 16(5):2395-2413.
• [14]McStay B, Grummt I: The epigenetics of rRNA genes: from molecular to chromosome biology. Annu Rev Cell Dev Biol 2008, 24:131-157.
• [15]Smirnov E, Cmarko D, Kováčik L, Hagen GM, Popov A, Raska O, Prieto JL, Ryabchenko B, Amim F, McStay B, Raska I: Replication timing of pseudo-NORs. J Struct Biol 2011, 173(2):213-218.
• [16]Cadet J, Mouret S, Ravanat JL, Douki T: Photoinduced damage to cellular DNA: direct and photosensitized reactions. Photochem Photobiol 2012, 88(5):1048-1065.
• [17]The Nuclear Protein Database [http://npd.hgu.mrc.ac.uk/user/ webcite]
• [18]Horáková AH, Bártová E, Galiová G, Uhlírová R, Matula P, Kozubek S: SUV39h-independent association of HP1β with fibrillarin-positive nucleolar regions. Chromosoma 2010, 119(3):227-241.
• [19]Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR: HP1-β mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008, 453(7195):682-686.
• [20]Luijsterburg MS, Dinant C, Lans H, Stap J, Wiernasz E, Lagerwerf S, Warmerdam DO, Lindh M, Brink MC, Dobrucki JW, Aten JA, Fousteri MI, Jansen G, Dantuma NP, Vermeulen W, Mullenders LH, Houtsmuller AB, Verschure PJ, van Driel R: Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol 2009, 185(4):577-586.
• [21]Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, Kashiwagi S, Fukami K, Miyata T, Miyoshi H, Imamura T, Ogawa M, Masai H, Miyawaki A: Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 2008, 132(3):487-498.
• [22]Stixová L, Hrušková T, Sehnalová P, Legartová S, Svidenská S, Kozubek S, Bártová E: Advanced microscopy techniques used for comparison of UVA- and γ-irradiation induced DNA damage in the cell nucleus and nucleolus. Folia Biol 2014, 60(Suppl 1):76-84.
• [23]Al-Baker EA, Oshin M, Hutchison CJ, Kill IR: Analysis of UV-induced damage and repair in young and senescent human dermal fibroblasts using the comet assay. Mech Ageing Dev 2005, 126(6–7):664-672.
• [24]Cioce M, Boulon S, Matera AG, Lamond AI: UV-induced fragmentation of Cajal bodies. J Cell Biol 2006, 175(3):401-413.
• [25]Daniely Y, Dimitrova DD, Borowiec JA: Stress-dependent nucleolin mobilization mediated by p53-nucleolin complex formation. Mol Cell Biol 2002, 22(16):6014-6022.
• [26]Chang MS, Sasaki H, Campbell MS, Kraeft SK, Sutherland R, Yang CY, Liu Y, Auclair D, Hao L, Sonoda H, Ferland LH, Chen LB: HRad17 colocalizes with NHP2L1 in the nucleolus and redistributes after UV irradiation. J Biol Chem 1999, 274(51):36544-36549.
• [27]Maiguel DA, Jones L, Chakravarty D, Yang C, Carrier F: Nucleophosmin sets a threshold for p53 response to UV radiation. Mol Cell Biol 2004, 24(9):3703-3711.
• [28]Nalabothula N, Carrier F: Cancer cells’ epigenetic composition and predisposition to histone deacetylase inhibitor sensitization. Epigenomics 2011, 3(2):145-155.
• [29]Popov A, Smirnov E, Kováčik L, Raška O, Hagen G, Stixová L, Raška I: Duration of the first steps of the human rRNA processing. Nucleus 2013, 4(2):134-141.
• [30]Roots R, Smith KC: Effects of actinomycin D on cell cycle kinetics and the DNA of Chinese hamster and mouse mammary tumor cells cultivated in vitro. Cancer Res 1976, 36(10):3654-3658.
• [31]Eppink B, Essers J, Kannar R: Interplay and quality of DNA damage repair mechanism. In Genome Organization and Function in the Cell Nucleus. Edited by Rippe K, Weinheim RK. Germany: Wiley-VCH; 2012:395-415.
• [32]Jackson SP, Bartek J: The DNA-damage response in human biology and disease. Nature 2009, 461(7267):1071-1078.
• [33]Dinant C, Luijsterburg MS: The emerging role of HP1 in the DNA damage response. Mol Cell Biol 2009, 29(24):6335-6340.
• [34]Zarebski M, Wiernasz E, Dobrucki JW: Recruitment of heterochromatin protein 1 to DNA repair sites. Cytometry A 2009, 75(7):619-625.
• [35]Moses RE, O’Malley BW: DNA transcription and repair: a confluence. J Biol Chem 2012, 287(28):23266-23270.
• [36]Yuan X, Feng W, Imhof A, Grummt I, Zhou Y: Activation of RNA polymerase I transcription by Cockayne syndrome group B protein and histone methyltransferase G9a. Mol Cell 2007, 27(4):585-595.
• [37]Ju BG, Lunyak VV, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MG: A topoisomerase IIβ-mediated dsDNA break required for regulated transcription. Science 2006, 312(5781):1798-1802.
• [38]Haffner MC, De Marzo AM, Meeker AK, Nelson WG, Yegnasubramanian S: Transcription-induced DNA double strand breaks: both oncogenic force and potential therapeutic target? Clin Cancer Res 2011, 17(12):b3858-b3864.
• [39]Zhang Y, Heermann DW: DNA double-strand breaks: linking gene expression to chromosome morphology and mobility. Chromosoma 2014, 123(1–2):103-115.
• [40]Bártová E, Šustáčková G, Stixová L, Kozubek S, Legartová S, Foltánková V: Recruitment of Oct4 protein to UV-damaged chromatin in embryonic stem cells. PLoS One 2011, 6(12):e27281.
• [41]Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M: Nucleolar proteome dynamics. Nature 2005, 433(7021):77-83.
• [42]Govoni M, Farabegoli F, Pession A, Novello F: Inhibition of topoisomerase II activity and its effect on nucleolar structure and function. Exp Cell Res 1994, 211(1):36-41.
• [43]Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Muller WG, McNally JG, Bazett-Jones DP, Nussenzweig A: Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J Cell Biol 2006, 172(6):823-834.
• [44]Bártová E, Galiová G, Krejcí J, Harnicarová A, Strasák L, Kozubek S: Epigenome and chromatin structure in human embryonic stem cells undergoing differentiation. Dev Dyn 2008, 237(12):3690-3702.
• [45]Sustáčková G, Kozubek S, Stixová L, Legartová S, Matula P, Orlova D, Bártová E: Acetylation-dependent nuclear arrangement and recruitment of BMI1 protein to UV-damaged chromatin. J Cell Physiol 2012, 227(5):1838-1850.
• [46]Iliakis G, Kurtzman S, Pantelias G, Okayasu R: Mechanism of radiosensitization by halogenated pyrimidines: effect of BrdU on radiation induction of DNA and chromosome damage and its correlation with cell killing. Radiat Res 1989, 119(2):286-304.
• [47]Lan L, Nakajima S, Komatsu K, Nussenzweig A, Shimamoto A, Oshima J, Yasui A: Accumulation of Werner protein at DNA double-strand breaks in human cells. J Cell Sci 2005, 118(18):4153-4162.
• [48]Stixová L, Matula P, Kozubek S, Gombitová A, Cmarko D, Raška I, Bártová E: Trajectories and nuclear arrangement of PML bodies are influenced by A-type lamin deficiency. Biol Cell 2012, 104(7):418-432.
• [49]Grueneberg DA, Pablo L, Hu KQ, August P, Weng Z, Papkoff J: A functional screen in human cells identifies UBF2 as an RNA polymerase II transcription factor that enhances the β-catenin signaling pathway. Mol Cell Biol 2003, 23(11):3936-3950.
• [50]Dawson MA, Bannister AJ, Gottgens B, Foster SD, Bartke T, Green AR, Kouzarides T: JAK2 phosphorylates histone H3Y41 and excludes HP1α from chromatin. Nature 2009, 461(7265):819-822.
• [51]Stixová L, Bártová E, Matula P, Daněk O, Legartová S, Kozubek S: Heterogeneity in the kinetics of nuclear proteins and trajectories of substructures associated with heterochromatin. Epigenetics Chromatin 2011, 4:5. BioMed Central Full Text
• [52]Piston DW, Kremers GJ: Fluorescent protein FRET: the good, the bad and the ugly. Trends Biochem Sci 2007, 32(9):407-414.
• [53]Matoušková P, Bártíková H, Boušová I, Hanušová V, Szotáková B, Skálová L: Reference genes for real-time PCR quantification of messenger RNAs and microRNAs in mouse model of obesity. PLoS One 2014, 9(1):e86033.